Accessing Sequence Resources

David M. Francis, The Ohio State University; Heather L. Merk, The Ohio State University

These webinars and the accompanying pdf (at the bottom of the page) were presented at the 2010 Tomato Disease Workshop. The videos provide overviews of available genome sequence resources for tomato, including NCBI, SWISS-PROT, EMBL, SGN, SolCAP, and the Gene Index Project. The final video provides an introduction to customized searches using the ENTREZ tool on NCBI.

In this video, Dr. Francis provides an overview of the SWISS-PROT (UniProt) database, which contains high quality annotation. In addition, information is non-redundant and cross-referenced with other databases.

In this video, Dr. Francis provides an overview of the tomato genome data available at the Solanaceae Genome Network (SGN). In addition, Dr. Francis describes the transcriptome sequence of tomato varieties that SolCAP has developed.

In this video, Dr. Francis provides an overview of resources developed by SolCAP. The resources for tomato include germplasm information, genotypic data, and phenotypic data. SolCAP has also developed searchable SNP datasets.

In this video, Dr. Francis provides an introduction to the ENTREZ tool for the NCBI database. He demonstrates how to use ENTREZ searches to acquire subsets of data that can be used in marker discovery. Dr. Francis performs sample searches to help users learn how to optimize database searches.

Funding Statement

Development of this lesson was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.